Those "numbers" are not rooted much in facts, because you avoided accounting for the Javelin's biggest strenght, that is, being able to shoot when the BW can't. So do this: take your dps numbers, and cut the BW's by 20%, to simulate the Javelin's ability to shoot more. Who's doing more damage now? 
And yes, while that number is obviously a rough estimate, I actually do shoot through cover a good amount of times. Remember that, since we were talking about the kishock, I gave an approximation of all the times I shoot through *any* sort of cover, even just shooting at corners for better RHA, or shooting through enemies themselves. That accounts for a lot of shots, for me.
About that last comment, the answer is the same I gave to your numbers above: how are you going to kill things faster than I am, if you can't shoot them at all?
The point is not about the Javelin's superior penetration, which is made a lot less important by all the penetration mods - it's about its scope, which effectively allows you to wallbang anything, anywhere you can actually hit with your amount of penetration. Better yet, it tells you if you can hit it or not. It's pretty awesome
And while the BW somewhat wallbangs too, it's limited to enemies whose position you can see - whether with your own eye, or with the scanner/HM/recon mine. And that is why the difference is also a lot kit and map dependant. On the DI, for example, that has recon mine and can spam it reasonably fast, the BW is without many doubts better. Same can be said if you play on a map like glacier, where the scanner is revealing pretty much any enemy you can shoot. But on something like... Say, Ghost? I, with a Javelin, can stay in one place (not that I'm going to, but still I could if I wanted to) and wallbang pretty much anything that appears anywhere on the map. Can you do the same with a BW? Nope. You're gonna have to go around to shoot, and you'll lose shot opportunities by doing so.
Besides, in all this discussion, we have not mentioned a slight, but important difference: the BW needs a headshot to get a OHK on shielded mooks (except on winfiltrators, and sometimes on them too), while the Javelin can kill anything by hitting their toe. And while with a good aim one can definitely make the BW faster at killing visible mooks than the Javelin is, you're gonna need an aimbot to get full leverage out of it and make the BW that 50% better at it that would come out of mere numbers.
Aedolon pretty much hit the point square on the nose; staying in one place - especially on higher difficulties (try plat) - is a great way to get yourself killed.
And you can stay in one spot with the Javelin, sure, but then what? You're just going to sit there and let the enemies come to you? Continuing off your "time spent moving is time spent not shooting" stance, it would seem then that while you're busy shooting enemies through walls/cover etc. the Black Widow user would be moving...into the line of site of more enemies/the next spawn. Guess who gets all of those? Not the Javelin guy who stayed in one place. This is especially true for the larger maps.
Those "numbers" are not rooted much in facts, because you avoided accounting for the Javelin's biggest strenght, that is, being able to shoot when the BW can't. So do this: take your dps numbers, and cut the BW's by 20%, to simulate the Javelin's ability to shoot more. Who's doing more damage now? 
And that's not how it works. You're bringing up specific circumstances in which a Javelin may be superior...but you fail to mention all the other times where it just simply isn't. In CQC (going off of Binary Helix), for example, the Javelin suffers where the BW doesn't. Quickscoping (if you're good at it) can also be done with the Javelin, but the RoF isn't nice to CQC situations whereas a Black Widow user will have an easier time killing things (this could qualify as a situation where a BW shoots more effectively when a Javelin can't...). Looking down a site line (which is the most common situation you'll find yourself in - also RHA) is another example - the BW will get more shots and/or kill more bosses/mooks.
There's also missing, which happens - sometimes a lot (depending on alcohol consumption

). A miss on a Black Widow is easily remedied, but if you miss with the Javelin (and there will be misses)? The Javelin definitely takes more skill, to be sure.
So while I agree that the Javelin does some things the BW can't (conversely, quickscoping and CQC are much better on the BW), I can't help but think that those situations aren't as common as you're making them out to be.
I'd like to be clear though, I do like the Javelin. I just think it's the
second best SR in the game